On the basis of morphologic and immunophenotypic studies, it is generally accepted that the lymphocyte population in thymomas is not neoplastic. We studied 10 thymomas with restriction endonuclease and Southern blot/DNA hybridization methods in an attempt to provide genotypic evidence in support of this hypothesis. The clinical, gross, and microscopic features of each case were reviewed and found to be entirely consistent with the diagnosis of thymoma. In addition to conventional histologic methods, we also studied each tumor by immunohistologic techniques. The lymphocytes generally had an immunotype characteristic of immature cortical thymocytes, and the epithelial cells were uniformly stained by antikeratin antibodies. DNA probes for the T-cell receptor beta-chain gene and immunoglobulin genes (C kappa, C lambda, and JH) were used in the genotypic studies. No gene rearrangements were detected in any of the thymomas. This study provides additional evidence that clonal proliferations of T or B lymphocytes are not present in thymomas; therefore, these cells are almost certainly not neoplastic. The results also provide a basis for the effective use of restriction endonuclease and Southern blot/DNA hybridization analysis in the differential diagnosis of non-Hodgkin's lymphoma and thymoma.